An image registration system for aligning first and second images. The novel system includes a first system for extracting a region of interest (ROI) from each image and a second system for coarsely aligning the regions of interest. The first system determines the size and location of the ROI based on the number of features contained within the region. The size of the ROI is enlarged until a number of features contained in the ROI is larger than a predetermined lower bound or until the size is greater than a predetermined upper bound. The second system computes a cross-correlation on the regions of interest using a plurality of transforms to find a coarse alignment transform having a highest correlation. The image registration system may also include a third system for performing sub-pixel alignment on the regions of interest.